Starting phenix.real_space_refine on Wed Aug 27 02:26:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h90_51946/08_2025/9h90_51946.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h90_51946/08_2025/9h90_51946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h90_51946/08_2025/9h90_51946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h90_51946/08_2025/9h90_51946.map" model { file = "/net/cci-nas-00/data/ceres_data/9h90_51946/08_2025/9h90_51946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h90_51946/08_2025/9h90_51946.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1509 5.49 5 S 59 5.16 5 C 23858 2.51 5 N 8845 2.21 5 O 13192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 47463 Number of models: 1 Model: "" Number of chains: 19 Chain: "u" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 526 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain breaks: 2 Chain: "C" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1580 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 944 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 2 Chain: "o" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "h" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 970 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "f" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 854 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "e" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1150 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "d" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1632 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain: "I" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "a" Number of atoms: 32388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1509, 32388 Classifications: {'RNA': 1509} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 81, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 193, 'rna3p': 1315} Chain breaks: 1 Chain: "t" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "r" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 446 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "q" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 632 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "p" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "l" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "k" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "D" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "J" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "a" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 27 Unusual residues: {'SCM': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 8.17, per 1000 atoms: 0.17 Number of scatterers: 47463 At special positions: 0 Unit cell: (194.163, 225.993, 165.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 1509 15.00 O 13192 8.00 N 8845 7.00 C 23858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 954.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3562 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 20 sheets defined 43.5% alpha, 22.6% beta 518 base pairs and 847 stacking pairs defined. Time for finding SS restraints: 9.02 Creating SS restraints... Processing helix chain 'u' and resid 12 through 25 Processing helix chain 'u' and resid 27 through 35 Processing helix chain 'u' and resid 40 through 62 removed outlier: 3.733A pdb=" N ALA u 61 " --> pdb=" O ALA u 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.810A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 3.744A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 84 through 96 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 116 through 121 removed outlier: 3.628A pdb=" N ALA G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.539A pdb=" N ASP G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 147 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'o' and resid 5 through 15 Processing helix chain 'o' and resid 24 through 46 removed outlier: 4.330A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.680A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 88 through 92 removed outlier: 3.649A pdb=" N LEU h 92 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 119 Processing helix chain 'f' and resid 14 through 32 removed outlier: 3.504A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.656A pdb=" N ILE f 71 " --> pdb=" O ASP f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 105 Processing helix chain 'e' and resid 56 through 71 Processing helix chain 'e' and resid 111 through 120 Processing helix chain 'e' and resid 133 through 148 removed outlier: 3.621A pdb=" N ARG e 139 " --> pdb=" O ILE e 135 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 158 Processing helix chain 'e' and resid 161 through 166 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.250A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 82 Processing helix chain 'd' and resid 85 through 96 Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 110 through 120 Processing helix chain 'd' and resid 148 through 151 removed outlier: 3.901A pdb=" N GLN d 151 " --> pdb=" O LYS d 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 148 through 151' Processing helix chain 'd' and resid 152 through 164 removed outlier: 3.582A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 204 removed outlier: 3.965A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 38 Processing helix chain 'I' and resid 41 through 55 Proline residue: I 50 - end of helix Processing helix chain 'I' and resid 70 through 90 Processing helix chain 'I' and resid 93 through 100 removed outlier: 3.615A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 42 removed outlier: 3.510A pdb=" N THR t 35 " --> pdb=" O TYR t 31 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 85 Processing helix chain 'r' and resid 25 through 30 Processing helix chain 'r' and resid 31 through 33 No H-bonds generated for 'chain 'r' and resid 31 through 33' Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 65 Processing helix chain 'p' and resid 53 through 62 Processing helix chain 'p' and resid 68 through 80 Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 117 Processing helix chain 'k' and resid 55 through 58 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.580A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 102 removed outlier: 3.736A pdb=" N VAL k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 29 removed outlier: 3.815A pdb=" N GLU D 10 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 51 removed outlier: 3.551A pdb=" N SER D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 5.313A pdb=" N ALA D 57 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER D 58 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'J' and resid 14 through 32 Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 21 removed outlier: 4.540A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 164 through 171 removed outlier: 5.797A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA4, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.673A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 24 through 28 Processing sheet with id=AA7, first strand: chain 'h' and resid 65 through 66 Processing sheet with id=AA8, first strand: chain 'h' and resid 75 through 77 Processing sheet with id=AA9, first strand: chain 'h' and resid 75 through 77 removed outlier: 6.710A pdb=" N ILE h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR h 128 " --> pdb=" O ILE h 101 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE h 101 " --> pdb=" O TYR h 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 36 through 51 removed outlier: 5.369A pdb=" N ILE f 36 " --> pdb=" O GLU f 65 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU f 65 " --> pdb=" O ILE f 36 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG f 44 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA f 57 " --> pdb=" O ARG f 44 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN f 46 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N HIS f 55 " --> pdb=" O GLN f 46 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 13 through 25 removed outlier: 5.262A pdb=" N GLU e 14 " --> pdb=" O GLY e 41 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY e 41 " --> pdb=" O GLU e 14 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU e 16 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL e 39 " --> pdb=" O LEU e 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 86 through 90 removed outlier: 6.949A pdb=" N ILE e 107 " --> pdb=" O SER e 126 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA e 128 " --> pdb=" O ILE e 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 128 through 129 removed outlier: 3.822A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 5 through 11 removed outlier: 5.918A pdb=" N ASN I 26 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL I 64 " --> pdb=" O ASN I 26 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL I 28 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL I 66 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'q' and resid 7 through 14 removed outlier: 17.187A pdb=" N THR q 7 " --> pdb=" O PHE q 28 " (cutoff:3.500A) removed outlier: 13.421A pdb=" N PHE q 28 " --> pdb=" O THR q 7 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLN q 9 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU q 26 " --> pdb=" O GLN q 9 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR q 22 " --> pdb=" O VAL q 13 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N TRP q 73 " --> pdb=" O LYS q 43 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N HIS q 45 " --> pdb=" O TRP q 73 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU q 75 " --> pdb=" O HIS q 45 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS q 47 " --> pdb=" O LEU q 75 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS q 77 " --> pdb=" O HIS q 47 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL q 76 " --> pdb=" O ALA q 62 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA q 62 " --> pdb=" O VAL q 76 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL q 78 " --> pdb=" O GLU q 60 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU q 60 " --> pdb=" O VAL q 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'p' and resid 50 through 52 removed outlier: 6.457A pdb=" N ILE p 19 " --> pdb=" O VAL p 36 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE p 38 " --> pdb=" O TYR p 17 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR p 17 " --> pdb=" O PHE p 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 30 through 40 removed outlier: 5.593A pdb=" N CYS l 34 " --> pdb=" O ARG l 56 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG l 56 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N TYR l 95 " --> pdb=" O GLU l 62 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR l 64 " --> pdb=" O TYR l 95 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR l 97 " --> pdb=" O THR l 64 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR l 66 " --> pdb=" O THR l 97 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ARG l 99 " --> pdb=" O TYR l 66 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLY l 100 " --> pdb=" O VAL l 79 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N VAL l 79 " --> pdb=" O GLY l 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.458A pdb=" N ALA k 41 " --> pdb=" O ASP k 36 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASP k 36 " --> pdb=" O ALA k 41 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY k 19 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N MET k 85 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA k 21 " --> pdb=" O MET k 85 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU k 82 " --> pdb=" O ILE k 107 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN k 109 " --> pdb=" O LEU k 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AC2, first strand: chain 'J' and resid 40 through 52 removed outlier: 4.327A pdb=" N LYS J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1288 hydrogen bonds 1978 hydrogen bond angles 0 basepair planarities 518 basepair parallelities 847 stacking parallelities Total time for adding SS restraints: 19.59 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6283 1.33 - 1.45: 22705 1.45 - 1.57: 19438 1.57 - 1.69: 3015 1.69 - 1.82: 104 Bond restraints: 51545 Sorted by residual: bond pdb=" CA SER o 35 " pdb=" CB SER o 35 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.55e-02 4.16e+03 2.26e+01 bond pdb=" CA SER e 126 " pdb=" CB SER e 126 " ideal model delta sigma weight residual 1.535 1.466 0.069 1.71e-02 3.42e+03 1.64e+01 bond pdb=" CA SER p 24 " pdb=" CB SER p 24 " ideal model delta sigma weight residual 1.529 1.465 0.063 1.64e-02 3.72e+03 1.49e+01 bond pdb=" NE ARG l 12 " pdb=" CZ ARG l 12 " ideal model delta sigma weight residual 1.326 1.284 0.042 1.10e-02 8.26e+03 1.43e+01 bond pdb=" NE ARG l 31 " pdb=" CZ ARG l 31 " ideal model delta sigma weight residual 1.326 1.285 0.041 1.10e-02 8.26e+03 1.40e+01 ... (remaining 51540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 73418 3.21 - 6.42: 3445 6.42 - 9.64: 181 9.64 - 12.85: 21 12.85 - 16.06: 2 Bond angle restraints: 77067 Sorted by residual: angle pdb=" O3' A a 584 " pdb=" P G a 585 " pdb=" O5' G a 585 " ideal model delta sigma weight residual 104.00 87.94 16.06 1.50e+00 4.44e-01 1.15e+02 angle pdb=" C4' A a 584 " pdb=" C3' A a 584 " pdb=" O3' A a 584 " ideal model delta sigma weight residual 113.00 99.60 13.40 1.50e+00 4.44e-01 7.98e+01 angle pdb=" O3' C a 18 " pdb=" P A a 19 " pdb=" O5' A a 19 " ideal model delta sigma weight residual 104.00 91.89 12.11 1.50e+00 4.44e-01 6.52e+01 angle pdb=" C4' U a 970 " pdb=" C3' U a 970 " pdb=" O3' U a 970 " ideal model delta sigma weight residual 109.40 121.44 -12.04 1.50e+00 4.44e-01 6.44e+01 angle pdb=" C4' A a 583 " pdb=" C3' A a 583 " pdb=" O3' A a 583 " ideal model delta sigma weight residual 113.00 101.04 11.96 1.50e+00 4.44e-01 6.36e+01 ... (remaining 77062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 29503 35.97 - 71.94: 3315 71.94 - 107.92: 258 107.92 - 143.89: 11 143.89 - 179.86: 17 Dihedral angle restraints: 33104 sinusoidal: 27589 harmonic: 5515 Sorted by residual: dihedral pdb=" CA LYS l 44 " pdb=" C LYS l 44 " pdb=" N PRO l 45 " pdb=" CA PRO l 45 " ideal model delta harmonic sigma weight residual 180.00 80.68 99.32 0 5.00e+00 4.00e-02 3.95e+02 dihedral pdb=" CA GLY J 38 " pdb=" C GLY J 38 " pdb=" N PRO J 39 " pdb=" CA PRO J 39 " ideal model delta harmonic sigma weight residual 180.00 -109.32 -70.68 0 5.00e+00 4.00e-02 2.00e+02 dihedral pdb=" C5' U a 448 " pdb=" C4' U a 448 " pdb=" C3' U a 448 " pdb=" O3' U a 448 " ideal model delta sinusoidal sigma weight residual 147.00 80.46 66.54 1 8.00e+00 1.56e-02 9.03e+01 ... (remaining 33101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 7171 0.118 - 0.235: 2594 0.235 - 0.353: 62 0.353 - 0.471: 5 0.471 - 0.589: 4 Chirality restraints: 9836 Sorted by residual: chirality pdb=" P U a 108 " pdb=" OP1 U a 108 " pdb=" OP2 U a 108 " pdb=" O5' U a 108 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.66e+00 chirality pdb=" P A a 1 " pdb=" OP1 A a 1 " pdb=" OP2 A a 1 " pdb=" O5' A a 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" C3' C a1410 " pdb=" C4' C a1410 " pdb=" O3' C a1410 " pdb=" C2' C a1410 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.52 2.00e-01 2.50e+01 6.88e+00 ... (remaining 9833 not shown) Planarity restraints: 4146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A a 651 " -0.125 2.00e-02 2.50e+03 5.22e-02 7.50e+01 pdb=" N9 A a 651 " 0.091 2.00e-02 2.50e+03 pdb=" C8 A a 651 " 0.023 2.00e-02 2.50e+03 pdb=" N7 A a 651 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A a 651 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A a 651 " -0.031 2.00e-02 2.50e+03 pdb=" N6 A a 651 " -0.017 2.00e-02 2.50e+03 pdb=" N1 A a 651 " -0.034 2.00e-02 2.50e+03 pdb=" C2 A a 651 " 0.012 2.00e-02 2.50e+03 pdb=" N3 A a 651 " 0.047 2.00e-02 2.50e+03 pdb=" C4 A a 651 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 62 " 0.676 9.50e-02 1.11e+02 3.04e-01 6.08e+01 pdb=" NE ARG d 62 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG d 62 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG d 62 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG d 62 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C a 893 " -0.106 2.00e-02 2.50e+03 4.96e-02 5.53e+01 pdb=" N1 C a 893 " 0.071 2.00e-02 2.50e+03 pdb=" C2 C a 893 " 0.029 2.00e-02 2.50e+03 pdb=" O2 C a 893 " 0.020 2.00e-02 2.50e+03 pdb=" N3 C a 893 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C a 893 " -0.035 2.00e-02 2.50e+03 pdb=" N4 C a 893 " -0.031 2.00e-02 2.50e+03 pdb=" C5 C a 893 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C a 893 " 0.048 2.00e-02 2.50e+03 ... (remaining 4143 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7805 2.77 - 3.30: 43848 3.30 - 3.83: 107638 3.83 - 4.37: 129476 4.37 - 4.90: 167607 Nonbonded interactions: 456374 Sorted by model distance: nonbonded pdb=" O2' U a 448 " pdb=" OP2 U a 449 " model vdw 2.234 3.040 nonbonded pdb=" O2' U a 353 " pdb=" O6 G a 356 " model vdw 2.336 3.040 nonbonded pdb=" OE1 GLU f 40 " pdb=" OG SER f 100 " model vdw 2.341 3.040 nonbonded pdb=" OP2 C a 532 " pdb=" OH TYR l 66 " model vdw 2.342 3.040 nonbonded pdb=" OP1 U a 62 " pdb=" O2' C a 395 " model vdw 2.351 3.040 ... (remaining 456369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 53.010 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 51545 Z= 0.581 Angle : 1.485 16.059 77067 Z= 0.940 Chirality : 0.100 0.589 9836 Planarity : 0.023 0.304 4146 Dihedral : 22.844 179.862 29542 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.91 % Allowed : 5.80 % Favored : 93.29 % Rotamer: Outliers : 2.56 % Allowed : 5.05 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (0.15), residues: 1878 helix: -2.87 (0.13), residues: 784 sheet: -1.96 (0.25), residues: 352 loop : -2.19 (0.19), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.005 ARG f 38 TYR 0.050 0.008 TYR I 6 PHE 0.033 0.006 PHE C 23 TRP 0.036 0.008 TRP p 60 HIS 0.019 0.004 HIS J 70 Details of bonding type rmsd covalent geometry : bond 0.00930 (51545) covalent geometry : angle 1.48464 (77067) hydrogen bonds : bond 0.16556 ( 2051) hydrogen bonds : angle 8.61087 ( 4198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 501 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: u 21 ARG cc_start: 0.5725 (mtt180) cc_final: 0.5078 (tpt170) REVERT: u 69 ARG cc_start: 0.3375 (OUTLIER) cc_final: 0.3014 (tpt170) REVERT: C 3 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5138 (mp-120) REVERT: C 36 ASP cc_start: 0.7905 (m-30) cc_final: 0.7459 (m-30) REVERT: C 41 GLN cc_start: 0.7815 (tt0) cc_final: 0.7594 (tp-100) REVERT: C 48 LYS cc_start: 0.6182 (mttt) cc_final: 0.5556 (ttpt) REVERT: C 93 LYS cc_start: 0.6886 (tttt) cc_final: 0.6571 (tmtt) REVERT: C 100 GLN cc_start: 0.6871 (mt0) cc_final: 0.5934 (mp10) REVERT: C 131 ARG cc_start: 0.7329 (mtt180) cc_final: 0.7025 (mtm-85) REVERT: C 132 ARG cc_start: 0.6901 (ttt180) cc_final: 0.6677 (mtt180) REVERT: C 135 LYS cc_start: 0.7396 (tttt) cc_final: 0.7164 (ttmt) REVERT: C 136 ARG cc_start: 0.7141 (ttt180) cc_final: 0.6819 (tpm170) REVERT: C 147 LYS cc_start: 0.8092 (mttt) cc_final: 0.7531 (mmtm) REVERT: C 157 LEU cc_start: 0.6624 (mt) cc_final: 0.6417 (mt) REVERT: G 97 ASN cc_start: 0.7037 (m-40) cc_final: 0.6819 (m-40) REVERT: G 102 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8018 (ttp80) REVERT: G 144 MET cc_start: 0.7501 (ttp) cc_final: 0.7241 (tpt) REVERT: o 47 LYS cc_start: 0.8684 (mttt) cc_final: 0.8407 (ttpp) REVERT: o 62 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.8065 (ttm170) REVERT: o 83 LYS cc_start: 0.8619 (tttt) cc_final: 0.8256 (ttpp) REVERT: o 84 ARG cc_start: 0.8863 (mtp180) cc_final: 0.8597 (mtm180) REVERT: o 88 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6424 (ttp80) REVERT: o 89 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.6058 (mmm-85) REVERT: h 8 SER cc_start: 0.9084 (t) cc_final: 0.8824 (m) REVERT: h 10 MET cc_start: 0.8900 (ttt) cc_final: 0.8544 (ttt) REVERT: h 26 LYS cc_start: 0.8799 (mttt) cc_final: 0.8189 (mppt) REVERT: h 64 LYS cc_start: 0.9143 (tttt) cc_final: 0.8883 (tttt) REVERT: h 91 GLN cc_start: 0.8321 (mt0) cc_final: 0.7884 (mm110) REVERT: h 94 SER cc_start: 0.8730 (m) cc_final: 0.8476 (t) REVERT: h 96 MET cc_start: 0.8832 (ttp) cc_final: 0.8573 (ttm) REVERT: h 118 LYS cc_start: 0.8179 (tttm) cc_final: 0.7734 (tptm) REVERT: f 2 ARG cc_start: 0.8411 (mtt180) cc_final: 0.8211 (mtt180) REVERT: f 31 GLU cc_start: 0.7585 (tt0) cc_final: 0.7262 (mt-10) REVERT: f 35 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6862 (mttp) REVERT: f 46 GLN cc_start: 0.7714 (tp40) cc_final: 0.7190 (tt0) REVERT: f 56 LYS cc_start: 0.8403 (mttt) cc_final: 0.8084 (mttt) REVERT: f 73 GLU cc_start: 0.7774 (tt0) cc_final: 0.7455 (mm-30) REVERT: f 102 MET cc_start: 0.8622 (mmt) cc_final: 0.8105 (mmp) REVERT: e 56 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7710 (mm-30) REVERT: e 66 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8095 (mm-30) REVERT: e 67 LYS cc_start: 0.8361 (tttt) cc_final: 0.8152 (mttp) REVERT: e 71 ASN cc_start: 0.7631 (m-40) cc_final: 0.7318 (t0) REVERT: e 89 ARG cc_start: 0.8860 (ttt180) cc_final: 0.8585 (ttp80) REVERT: e 94 LYS cc_start: 0.8772 (mttt) cc_final: 0.8371 (mtpt) REVERT: e 102 GLU cc_start: 0.8553 (tt0) cc_final: 0.7951 (mp0) REVERT: e 149 LYS cc_start: 0.8793 (mttt) cc_final: 0.8516 (mtmm) REVERT: d 50 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: d 57 GLU cc_start: 0.8663 (tp30) cc_final: 0.8419 (tp30) REVERT: d 73 ARG cc_start: 0.8343 (ttt180) cc_final: 0.7540 (ttm-80) REVERT: d 78 GLU cc_start: 0.8304 (tt0) cc_final: 0.8104 (tp30) REVERT: d 95 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8668 (mm-30) REVERT: d 131 ASN cc_start: 0.8842 (p0) cc_final: 0.8571 (p0) REVERT: d 136 LYS cc_start: 0.8465 (mttt) cc_final: 0.8116 (tttm) REVERT: d 152 GLN cc_start: 0.8493 (mt0) cc_final: 0.8058 (mt0) REVERT: d 163 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6301 (mm-30) REVERT: d 172 GLU cc_start: 0.7300 (tt0) cc_final: 0.7068 (tm-30) REVERT: d 183 LYS cc_start: 0.7246 (mttt) cc_final: 0.6660 (ttpp) REVERT: d 206 LYS cc_start: 0.7488 (tttm) cc_final: 0.6900 (tmtm) REVERT: I 45 MET cc_start: 0.5517 (mpp) cc_final: 0.4773 (ttp) REVERT: I 72 SER cc_start: 0.7941 (t) cc_final: 0.7740 (m) REVERT: I 79 ARG cc_start: 0.8062 (ttp-170) cc_final: 0.7840 (ttp80) REVERT: t 8 LYS cc_start: 0.8736 (tttt) cc_final: 0.8481 (ttmt) REVERT: t 25 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8283 (ttp-170) REVERT: t 76 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7985 (mtmm) REVERT: t 84 LYS cc_start: 0.6856 (tttt) cc_final: 0.5544 (mmpt) REVERT: r 35 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7754 (tp30) REVERT: q 11 ARG cc_start: 0.8149 (ttt180) cc_final: 0.7654 (ttm-80) REVERT: q 16 LYS cc_start: 0.7960 (mttt) cc_final: 0.7619 (mttm) REVERT: q 26 GLU cc_start: 0.8476 (tt0) cc_final: 0.8224 (mm-30) REVERT: q 40 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7883 (mtp85) REVERT: q 55 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7564 (mt) REVERT: q 57 ASP cc_start: 0.8589 (m-30) cc_final: 0.8387 (m-30) REVERT: q 77 LYS cc_start: 0.7153 (tttt) cc_final: 0.6880 (ttpt) REVERT: q 81 LYS cc_start: 0.6747 (mttt) cc_final: 0.6464 (tptt) REVERT: p 44 LYS cc_start: 0.7242 (mttt) cc_final: 0.6987 (mptp) REVERT: p 73 LYS cc_start: 0.8388 (mptt) cc_final: 0.8031 (tppp) REVERT: l 14 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7384 (mmtm) REVERT: l 39 THR cc_start: 0.8638 (p) cc_final: 0.8392 (m) REVERT: l 43 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7321 (tttp) REVERT: l 44 LYS cc_start: 0.7994 (mttt) cc_final: 0.7687 (mmtp) REVERT: l 56 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7840 (ttm-80) REVERT: l 75 GLN cc_start: 0.8361 (mt0) cc_final: 0.7935 (mp10) REVERT: l 82 ILE cc_start: 0.8975 (pt) cc_final: 0.8614 (mp) REVERT: l 94 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7619 (mtp180) REVERT: k 40 ASN cc_start: 0.7860 (m-40) cc_final: 0.7653 (m110) REVERT: k 73 MET cc_start: 0.6921 (mtp) cc_final: 0.6582 (ttp) REVERT: k 98 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7408 (mtp85) REVERT: k 108 THR cc_start: 0.7514 (p) cc_final: 0.7051 (p) REVERT: k 126 LYS cc_start: 0.7841 (tttt) cc_final: 0.7266 (mmmt) REVERT: D 89 MET cc_start: 0.8685 (mmt) cc_final: 0.8091 (mmp) REVERT: J 37 ARG cc_start: 0.5876 (ttt180) cc_final: 0.5490 (ttm110) REVERT: J 46 LYS cc_start: 0.8579 (mttt) cc_final: 0.8326 (mtmp) REVERT: J 72 ARG cc_start: 0.7693 (mmt-90) cc_final: 0.7451 (mmt90) outliers start: 40 outliers final: 6 residues processed: 523 average time/residue: 0.8765 time to fit residues: 546.5872 Evaluate side-chains 419 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 404 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 69 ARG Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 56 HIS G 68 ASN o 40 GLN f 14 GLN f 17 GLN f 87 ASN e 78 ASN e 90 HIS e 98 GLN I 125 GLN t 20 HIS l 96 HIS k 29 ASN D 49 GLN D 60 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.139088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.118335 restraints weight = 53267.276| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 0.93 r_work: 0.2781 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 51545 Z= 0.458 Angle : 0.841 10.432 77067 Z= 0.426 Chirality : 0.050 0.371 9836 Planarity : 0.008 0.099 4146 Dihedral : 23.827 177.522 25809 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.01 % Rotamer: Outliers : 5.24 % Allowed : 12.92 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.18), residues: 1878 helix: -0.61 (0.17), residues: 790 sheet: -1.31 (0.25), residues: 354 loop : -1.48 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG l 110 TYR 0.027 0.003 TYR q 34 PHE 0.019 0.003 PHE t 51 TRP 0.021 0.003 TRP C 201 HIS 0.007 0.002 HIS f 11 Details of bonding type rmsd covalent geometry : bond 0.00891 (51545) covalent geometry : angle 0.84054 (77067) hydrogen bonds : bond 0.07456 ( 2051) hydrogen bonds : angle 4.06739 ( 4198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 397 time to evaluate : 0.891 Fit side-chains REVERT: u 17 ARG cc_start: 0.6028 (ttp-170) cc_final: 0.5746 (ttm-80) REVERT: u 18 ARG cc_start: 0.6662 (ttp-110) cc_final: 0.6156 (ttp-110) REVERT: u 21 ARG cc_start: 0.6315 (mtt180) cc_final: 0.6023 (ttt180) REVERT: u 55 ARG cc_start: 0.6056 (ttm110) cc_final: 0.5389 (ttp80) REVERT: u 69 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.5346 (tpt170) REVERT: C 48 LYS cc_start: 0.6694 (mttt) cc_final: 0.6093 (ttpt) REVERT: C 93 LYS cc_start: 0.7164 (tttt) cc_final: 0.6821 (tmtt) REVERT: C 147 LYS cc_start: 0.8183 (mttt) cc_final: 0.7796 (mmtp) REVERT: G 76 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7314 (mtmm) REVERT: G 97 ASN cc_start: 0.7353 (m-40) cc_final: 0.7132 (m-40) REVERT: o 84 ARG cc_start: 0.8808 (mtp180) cc_final: 0.8514 (mtm180) REVERT: h 26 LYS cc_start: 0.8381 (mttt) cc_final: 0.8134 (mppt) REVERT: f 35 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7150 (mttp) REVERT: e 69 ARG cc_start: 0.8315 (mtt180) cc_final: 0.8105 (mtt90) REVERT: d 124 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8525 (mt) REVERT: d 148 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7248 (mtpp) REVERT: d 152 GLN cc_start: 0.8912 (mt0) cc_final: 0.8598 (mt0) REVERT: d 206 LYS cc_start: 0.7489 (tttm) cc_final: 0.7132 (tptt) REVERT: I 35 ASP cc_start: 0.6452 (m-30) cc_final: 0.6182 (m-30) REVERT: I 45 MET cc_start: 0.5992 (mpp) cc_final: 0.4821 (ttp) REVERT: r 38 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8061 (mmmm) REVERT: q 55 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7477 (mt) REVERT: q 77 LYS cc_start: 0.7773 (tttt) cc_final: 0.7522 (ttpt) REVERT: l 43 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7460 (tttm) REVERT: l 94 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7596 (mtp180) REVERT: k 75 LYS cc_start: 0.8073 (mttt) cc_final: 0.7846 (mttm) REVERT: k 126 LYS cc_start: 0.8104 (tttt) cc_final: 0.7708 (mmmt) REVERT: D 13 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6798 (mtt90) REVERT: D 89 MET cc_start: 0.9000 (mmt) cc_final: 0.8630 (mmp) REVERT: J 42 LEU cc_start: 0.8679 (mt) cc_final: 0.8440 (mt) outliers start: 82 outliers final: 41 residues processed: 441 average time/residue: 0.8367 time to fit residues: 439.4262 Evaluate side-chains 412 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 69 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain e residue 13 GLN Chi-restraints excluded: chain e residue 15 LYS Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 126 SER Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 157 LYS Chi-restraints excluded: chain e residue 166 SER Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 148 LYS Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain r residue 38 LYS Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 27 ARG Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain l residue 17 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 56 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 331 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 314 optimal weight: 0.0040 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 100 GLN G 68 ASN G 142 HIS h 91 GLN f 14 GLN f 46 GLN e 78 ASN d 116 GLN k 109 ASN D 4 ASN D 49 GLN J 56 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124668 restraints weight = 52821.519| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 0.65 r_work: 0.2881 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 51545 Z= 0.177 Angle : 0.581 10.942 77067 Z= 0.306 Chirality : 0.036 0.329 9836 Planarity : 0.005 0.069 4146 Dihedral : 23.633 179.086 25793 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.91 % Rotamer: Outliers : 4.54 % Allowed : 16.75 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.19), residues: 1878 helix: 0.75 (0.18), residues: 792 sheet: -0.82 (0.27), residues: 351 loop : -1.08 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG q 40 TYR 0.020 0.002 TYR I 6 PHE 0.011 0.001 PHE d 182 TRP 0.016 0.001 TRP C 201 HIS 0.003 0.001 HIS k 24 Details of bonding type rmsd covalent geometry : bond 0.00336 (51545) covalent geometry : angle 0.58140 (77067) hydrogen bonds : bond 0.05583 ( 2051) hydrogen bonds : angle 3.52794 ( 4198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 366 time to evaluate : 0.747 Fit side-chains REVERT: u 17 ARG cc_start: 0.6062 (ttp-170) cc_final: 0.5784 (ttm-80) REVERT: u 18 ARG cc_start: 0.6834 (ttp-110) cc_final: 0.6374 (ttp-110) REVERT: u 21 ARG cc_start: 0.6586 (mtt180) cc_final: 0.6228 (tpt170) REVERT: u 45 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7915 (mtm-85) REVERT: C 48 LYS cc_start: 0.6681 (mttt) cc_final: 0.6116 (ttpt) REVERT: C 85 GLU cc_start: 0.7272 (tp30) cc_final: 0.6869 (tm-30) REVERT: C 93 LYS cc_start: 0.7153 (tttt) cc_final: 0.6874 (tmtt) REVERT: C 100 GLN cc_start: 0.7086 (mt0) cc_final: 0.6282 (mp10) REVERT: C 131 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7306 (mtt90) REVERT: C 147 LYS cc_start: 0.8186 (mttt) cc_final: 0.7877 (mmtm) REVERT: G 130 ASN cc_start: 0.6961 (m-40) cc_final: 0.6690 (m110) REVERT: o 40 GLN cc_start: 0.8456 (mm110) cc_final: 0.8195 (mm110) REVERT: o 83 LYS cc_start: 0.8674 (tttt) cc_final: 0.8194 (ttpt) REVERT: o 84 ARG cc_start: 0.8689 (mtp180) cc_final: 0.8453 (mtm180) REVERT: h 26 LYS cc_start: 0.8299 (mttt) cc_final: 0.8086 (mppt) REVERT: f 9 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8379 (mpp) REVERT: f 35 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7118 (mttp) REVERT: f 73 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7469 (mm-30) REVERT: f 93 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7593 (mtpp) REVERT: d 50 GLU cc_start: 0.8386 (mp0) cc_final: 0.7782 (tp30) REVERT: d 152 GLN cc_start: 0.8785 (mt0) cc_final: 0.8544 (mt0) REVERT: d 177 LYS cc_start: 0.6912 (mtpt) cc_final: 0.6462 (ttmt) REVERT: d 206 LYS cc_start: 0.7204 (tttm) cc_final: 0.6927 (tptt) REVERT: I 45 MET cc_start: 0.5985 (mpp) cc_final: 0.4840 (ttp) REVERT: t 36 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8220 (t) REVERT: q 55 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7403 (mt) REVERT: q 77 LYS cc_start: 0.7680 (tttt) cc_final: 0.7473 (ttpt) REVERT: p 73 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8031 (tppt) REVERT: l 43 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7558 (tttt) REVERT: k 126 LYS cc_start: 0.8105 (tttt) cc_final: 0.7731 (mmmt) REVERT: k 128 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8205 (mtm-85) REVERT: D 24 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7873 (ttt180) REVERT: D 61 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7614 (tpt170) REVERT: D 89 MET cc_start: 0.8882 (mmt) cc_final: 0.8446 (mmp) outliers start: 71 outliers final: 32 residues processed: 404 average time/residue: 0.8386 time to fit residues: 406.5422 Evaluate side-chains 378 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 339 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain e residue 13 GLN Chi-restraints excluded: chain e residue 94 LYS Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 27 ARG Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain p residue 73 LYS Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 306 optimal weight: 0.2980 chunk 185 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 68 ASN G 153 HIS o 40 GLN h 91 GLN f 14 GLN e 13 GLN e 78 ASN e 98 GLN d 116 GLN l 72 HIS k 109 ASN D 4 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.142972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.117622 restraints weight = 53000.556| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 0.51 r_work: 0.2899 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 51545 Z= 0.277 Angle : 0.654 7.623 77067 Z= 0.338 Chirality : 0.040 0.310 9836 Planarity : 0.006 0.065 4146 Dihedral : 23.650 178.935 25788 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 5.75 % Allowed : 17.33 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.19), residues: 1878 helix: 0.88 (0.18), residues: 788 sheet: -0.68 (0.26), residues: 348 loop : -0.92 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG o 64 TYR 0.020 0.002 TYR I 6 PHE 0.014 0.002 PHE d 135 TRP 0.016 0.002 TRP C 201 HIS 0.005 0.001 HIS k 24 Details of bonding type rmsd covalent geometry : bond 0.00534 (51545) covalent geometry : angle 0.65398 (77067) hydrogen bonds : bond 0.06208 ( 2051) hydrogen bonds : angle 3.51851 ( 4198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 347 time to evaluate : 0.738 Fit side-chains REVERT: u 7 ARG cc_start: 0.4033 (OUTLIER) cc_final: 0.3486 (tpm170) REVERT: u 17 ARG cc_start: 0.6106 (ttp-170) cc_final: 0.5477 (ttm-80) REVERT: u 21 ARG cc_start: 0.6657 (mtt180) cc_final: 0.5642 (mmt-90) REVERT: u 45 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8093 (mtm-85) REVERT: C 48 LYS cc_start: 0.6744 (mttt) cc_final: 0.6071 (ttpt) REVERT: C 49 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6191 (ptpt) REVERT: C 93 LYS cc_start: 0.7185 (tttt) cc_final: 0.6816 (tmtt) REVERT: C 100 GLN cc_start: 0.7127 (mt0) cc_final: 0.6313 (mp10) REVERT: C 131 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7316 (mtt90) REVERT: C 147 LYS cc_start: 0.8175 (mttt) cc_final: 0.7873 (mttp) REVERT: G 68 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7298 (t0) REVERT: G 76 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7227 (mtmm) REVERT: G 79 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.6059 (mmm160) REVERT: G 116 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.4588 (tmt) REVERT: G 120 LEU cc_start: 0.7807 (tp) cc_final: 0.7528 (tp) REVERT: o 83 LYS cc_start: 0.8628 (tttt) cc_final: 0.8136 (ttpt) REVERT: o 84 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8470 (mtm180) REVERT: h 26 LYS cc_start: 0.8288 (mttt) cc_final: 0.8077 (mppt) REVERT: h 80 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8591 (mtp180) REVERT: h 110 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8604 (mp) REVERT: f 9 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8448 (mpp) REVERT: f 35 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7131 (mttp) REVERT: f 73 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7488 (tp30) REVERT: f 91 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7260 (mmm160) REVERT: f 93 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7585 (mtpp) REVERT: e 69 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7845 (mtt90) REVERT: d 50 GLU cc_start: 0.8369 (mp0) cc_final: 0.7759 (tp30) REVERT: d 152 GLN cc_start: 0.8848 (mt0) cc_final: 0.8558 (mt0) REVERT: d 206 LYS cc_start: 0.7305 (tttm) cc_final: 0.6901 (tptt) REVERT: I 45 MET cc_start: 0.5805 (tpp) cc_final: 0.4685 (ttp) REVERT: t 36 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8197 (t) REVERT: q 55 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7465 (mt) REVERT: p 73 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7990 (tppt) REVERT: l 43 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7475 (tttt) REVERT: l 44 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6581 (mmtp) REVERT: l 94 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7864 (mtt180) REVERT: k 126 LYS cc_start: 0.7945 (tttt) cc_final: 0.7593 (mmmt) REVERT: D 24 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7863 (ttt180) REVERT: D 61 ARG cc_start: 0.7922 (tpt90) cc_final: 0.7695 (tpt170) REVERT: D 89 MET cc_start: 0.8891 (mmt) cc_final: 0.8453 (mmp) outliers start: 90 outliers final: 47 residues processed: 395 average time/residue: 0.8195 time to fit residues: 389.4842 Evaluate side-chains 401 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 336 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 7 ARG Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 68 ASN Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain h residue 110 LEU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain e residue 13 GLN Chi-restraints excluded: chain e residue 15 LYS Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 94 LYS Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 149 LYS Chi-restraints excluded: chain e residue 166 SER Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 27 ARG Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain p residue 73 LYS Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain J residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 91 optimal weight: 0.0870 chunk 123 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 85 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 chunk 296 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 153 HIS f 14 GLN f 99 GLN e 78 ASN d 116 GLN k 22 HIS D 4 ASN D 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.150109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.123933 restraints weight = 53388.911| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 0.44 r_work: 0.3016 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 51545 Z= 0.124 Angle : 0.528 7.668 77067 Z= 0.279 Chirality : 0.033 0.319 9836 Planarity : 0.004 0.065 4146 Dihedral : 23.511 179.654 25787 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.29 % Favored : 97.55 % Rotamer: Outliers : 4.16 % Allowed : 18.99 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.19), residues: 1878 helix: 1.44 (0.18), residues: 792 sheet: -0.57 (0.26), residues: 355 loop : -0.75 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 118 TYR 0.016 0.001 TYR I 6 PHE 0.009 0.001 PHE o 43 TRP 0.015 0.001 TRP C 201 HIS 0.003 0.001 HIS e 90 Details of bonding type rmsd covalent geometry : bond 0.00230 (51545) covalent geometry : angle 0.52835 (77067) hydrogen bonds : bond 0.05100 ( 2051) hydrogen bonds : angle 3.22933 ( 4198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 0.781 Fit side-chains REVERT: u 17 ARG cc_start: 0.6039 (ttp-170) cc_final: 0.5398 (ttm-80) REVERT: u 21 ARG cc_start: 0.6538 (mtt180) cc_final: 0.5578 (mtt180) REVERT: u 45 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7964 (mtm-85) REVERT: C 49 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.6252 (ptpt) REVERT: C 93 LYS cc_start: 0.7233 (tttt) cc_final: 0.6817 (tmtt) REVERT: C 100 GLN cc_start: 0.6988 (mt0) cc_final: 0.6254 (mp10) REVERT: C 131 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7238 (mtt90) REVERT: C 147 LYS cc_start: 0.8111 (mttt) cc_final: 0.7818 (mttp) REVERT: G 116 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5895 (tmt) REVERT: o 83 LYS cc_start: 0.8544 (tttt) cc_final: 0.8008 (ttpt) REVERT: o 84 ARG cc_start: 0.8636 (mtp180) cc_final: 0.8411 (mtm180) REVERT: f 9 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8416 (mpp) REVERT: f 35 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7081 (mttp) REVERT: f 73 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7445 (tp30) REVERT: f 93 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7459 (mtpp) REVERT: f 102 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7546 (mmt) REVERT: d 50 GLU cc_start: 0.8274 (mp0) cc_final: 0.7687 (tp30) REVERT: d 206 LYS cc_start: 0.7230 (tttm) cc_final: 0.6805 (tmtm) REVERT: I 45 MET cc_start: 0.5792 (tpp) cc_final: 0.4683 (ttp) REVERT: t 36 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8218 (t) REVERT: q 55 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7402 (mt) REVERT: l 40 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (p) REVERT: l 43 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7318 (tttt) REVERT: l 44 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6330 (mmtp) REVERT: l 62 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: l 94 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7811 (mtt180) REVERT: k 126 LYS cc_start: 0.7943 (tttt) cc_final: 0.7613 (mmmt) REVERT: D 24 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7677 (ttt180) REVERT: D 89 MET cc_start: 0.8822 (mmt) cc_final: 0.8507 (mmt) outliers start: 65 outliers final: 22 residues processed: 387 average time/residue: 0.8074 time to fit residues: 374.5791 Evaluate side-chains 365 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 330 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 166 SER Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 275 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 148 ASN G 153 HIS o 40 GLN h 91 GLN f 14 GLN f 99 GLN e 78 ASN e 98 GLN d 116 GLN I 125 GLN t 75 HIS k 109 ASN D 4 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.141669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.122159 restraints weight = 52779.297| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.81 r_work: 0.2853 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 51545 Z= 0.374 Angle : 0.732 7.645 77067 Z= 0.371 Chirality : 0.044 0.330 9836 Planarity : 0.006 0.058 4146 Dihedral : 23.632 179.998 25785 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer: Outliers : 5.18 % Allowed : 19.18 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.19), residues: 1878 helix: 1.02 (0.18), residues: 784 sheet: -0.55 (0.26), residues: 353 loop : -0.73 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 44 TYR 0.020 0.003 TYR I 6 PHE 0.018 0.002 PHE o 43 TRP 0.015 0.003 TRP C 201 HIS 0.006 0.001 HIS k 24 Details of bonding type rmsd covalent geometry : bond 0.00727 (51545) covalent geometry : angle 0.73236 (77067) hydrogen bonds : bond 0.06719 ( 2051) hydrogen bonds : angle 3.51350 ( 4198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 345 time to evaluate : 0.732 Fit side-chains REVERT: u 17 ARG cc_start: 0.6117 (ttp-170) cc_final: 0.5420 (ttp80) REVERT: u 21 ARG cc_start: 0.6696 (mtt180) cc_final: 0.5896 (mmt90) REVERT: u 69 ARG cc_start: 0.5213 (OUTLIER) cc_final: 0.4896 (tpp-160) REVERT: C 93 LYS cc_start: 0.7214 (tttt) cc_final: 0.7011 (tmtt) REVERT: C 100 GLN cc_start: 0.7114 (mt0) cc_final: 0.6487 (mp10) REVERT: C 131 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7307 (mtt90) REVERT: C 147 LYS cc_start: 0.8104 (mttt) cc_final: 0.7810 (mttp) REVERT: G 79 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.6146 (mmm160) REVERT: G 116 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.4788 (tmt) REVERT: o 84 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8388 (mtm180) REVERT: h 80 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8681 (mtp180) REVERT: f 9 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8303 (mpp) REVERT: f 35 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7223 (mttp) REVERT: d 50 GLU cc_start: 0.8200 (mp0) cc_final: 0.7746 (tp30) REVERT: d 124 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8547 (mt) REVERT: d 183 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7147 (ttpp) REVERT: d 206 LYS cc_start: 0.7312 (tttm) cc_final: 0.7021 (tmtm) REVERT: I 45 MET cc_start: 0.5822 (tpp) cc_final: 0.4801 (ttp) REVERT: I 93 LEU cc_start: 0.7885 (mt) cc_final: 0.7129 (tt) REVERT: I 125 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: t 36 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8339 (t) REVERT: q 55 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7561 (mt) REVERT: l 40 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8753 (p) REVERT: l 43 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7513 (tttt) REVERT: l 44 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6694 (mmtp) REVERT: k 82 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6756 (mt) REVERT: k 126 LYS cc_start: 0.7989 (tttt) cc_final: 0.7718 (mmmt) REVERT: D 89 MET cc_start: 0.8933 (mmt) cc_final: 0.8506 (mmp) outliers start: 81 outliers final: 45 residues processed: 388 average time/residue: 0.7169 time to fit residues: 334.3573 Evaluate side-chains 391 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 332 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 69 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 2 SER Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain l residue 17 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 256 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 153 HIS o 40 GLN h 91 GLN f 14 GLN f 99 GLN e 78 ASN d 92 GLN d 116 GLN t 75 HIS k 109 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.142914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123181 restraints weight = 52641.616| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.75 r_work: 0.2830 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 51545 Z= 0.297 Angle : 0.666 7.624 77067 Z= 0.342 Chirality : 0.041 0.308 9836 Planarity : 0.005 0.060 4146 Dihedral : 23.617 179.367 25785 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.91 % Rotamer: Outliers : 5.56 % Allowed : 19.88 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.19), residues: 1878 helix: 1.01 (0.18), residues: 784 sheet: -0.59 (0.26), residues: 361 loop : -0.70 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 118 TYR 0.019 0.002 TYR I 6 PHE 0.016 0.002 PHE o 43 TRP 0.017 0.002 TRP C 201 HIS 0.006 0.001 HIS t 75 Details of bonding type rmsd covalent geometry : bond 0.00575 (51545) covalent geometry : angle 0.66628 (77067) hydrogen bonds : bond 0.06308 ( 2051) hydrogen bonds : angle 3.46429 ( 4198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 335 time to evaluate : 0.574 Fit side-chains REVERT: u 17 ARG cc_start: 0.5982 (ttp-170) cc_final: 0.5097 (ttp80) REVERT: u 21 ARG cc_start: 0.6489 (mtt180) cc_final: 0.5708 (mmt90) REVERT: u 45 ARG cc_start: 0.8281 (mtp180) cc_final: 0.8072 (mtm-85) REVERT: u 69 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.4643 (tpp-160) REVERT: C 93 LYS cc_start: 0.7366 (tttt) cc_final: 0.6952 (tmtt) REVERT: C 100 GLN cc_start: 0.7055 (mt0) cc_final: 0.6180 (mp10) REVERT: C 131 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7225 (mtt90) REVERT: C 147 LYS cc_start: 0.8151 (mttt) cc_final: 0.7823 (mttp) REVERT: G 79 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.6026 (mmm160) REVERT: G 116 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.4460 (tmt) REVERT: o 83 LYS cc_start: 0.8651 (tttt) cc_final: 0.8130 (ttpt) REVERT: o 84 ARG cc_start: 0.8696 (mtp180) cc_final: 0.8413 (mtm180) REVERT: h 80 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8607 (mtp180) REVERT: f 9 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8290 (mpp) REVERT: f 35 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7123 (mttp) REVERT: f 91 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.6857 (mmm160) REVERT: d 50 GLU cc_start: 0.8300 (mp0) cc_final: 0.7715 (tp30) REVERT: d 124 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8569 (mt) REVERT: d 183 LYS cc_start: 0.7914 (mmmt) cc_final: 0.6946 (ttpp) REVERT: d 206 LYS cc_start: 0.7405 (tttm) cc_final: 0.7039 (tmtm) REVERT: I 45 MET cc_start: 0.5722 (tpp) cc_final: 0.4643 (ttp) REVERT: I 125 GLN cc_start: 0.8198 (tt0) cc_final: 0.7974 (mt0) REVERT: t 36 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8205 (t) REVERT: r 38 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8729 (mtmm) REVERT: q 55 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7550 (mt) REVERT: l 43 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7411 (tttt) REVERT: l 44 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6660 (mmtp) REVERT: k 82 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6764 (mt) REVERT: k 126 LYS cc_start: 0.7986 (tttt) cc_final: 0.7626 (mmmt) REVERT: D 89 MET cc_start: 0.8882 (mmt) cc_final: 0.8455 (mmp) outliers start: 87 outliers final: 53 residues processed: 385 average time/residue: 0.6078 time to fit residues: 282.5664 Evaluate side-chains 392 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 325 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 69 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 2 SER Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 149 LYS Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 38 LYS Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain l residue 17 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain J residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 46 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 307 optimal weight: 0.5980 chunk 324 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 153 HIS o 40 GLN h 91 GLN f 14 GLN f 99 GLN e 13 GLN e 78 ASN e 98 GLN d 116 GLN I 125 GLN ** t 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 109 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.142821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.116071 restraints weight = 52907.566| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 0.52 r_work: 0.2911 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 51545 Z= 0.267 Angle : 0.644 7.671 77067 Z= 0.333 Chirality : 0.039 0.298 9836 Planarity : 0.005 0.061 4146 Dihedral : 23.622 179.340 25785 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.19 % Favored : 96.65 % Rotamer: Outliers : 5.75 % Allowed : 19.50 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.19), residues: 1878 helix: 1.04 (0.18), residues: 786 sheet: -0.56 (0.26), residues: 361 loop : -0.71 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 127 TYR 0.025 0.002 TYR f 4 PHE 0.016 0.002 PHE o 43 TRP 0.017 0.002 TRP C 201 HIS 0.004 0.001 HIS k 24 Details of bonding type rmsd covalent geometry : bond 0.00515 (51545) covalent geometry : angle 0.64397 (77067) hydrogen bonds : bond 0.06250 ( 2051) hydrogen bonds : angle 3.45536 ( 4198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 333 time to evaluate : 1.216 Fit side-chains REVERT: u 7 ARG cc_start: 0.3791 (OUTLIER) cc_final: 0.3219 (tpm170) REVERT: u 17 ARG cc_start: 0.5987 (ttp-170) cc_final: 0.5073 (ttp80) REVERT: u 21 ARG cc_start: 0.6460 (mtt180) cc_final: 0.5691 (mmt90) REVERT: u 45 ARG cc_start: 0.8285 (mtp180) cc_final: 0.8081 (mtm-85) REVERT: u 69 ARG cc_start: 0.4999 (OUTLIER) cc_final: 0.4677 (tpp-160) REVERT: C 93 LYS cc_start: 0.7355 (tttt) cc_final: 0.6943 (tmtt) REVERT: C 100 GLN cc_start: 0.7096 (mt0) cc_final: 0.6244 (mp10) REVERT: C 131 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7293 (mtt90) REVERT: C 147 LYS cc_start: 0.8144 (mttt) cc_final: 0.7826 (mttp) REVERT: G 79 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.6021 (mmm160) REVERT: G 116 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.4454 (tmt) REVERT: o 83 LYS cc_start: 0.8642 (tttt) cc_final: 0.8113 (ttpt) REVERT: o 84 ARG cc_start: 0.8718 (mtp180) cc_final: 0.8441 (mtm180) REVERT: h 8 SER cc_start: 0.9308 (p) cc_final: 0.8815 (m) REVERT: h 80 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8573 (mtp180) REVERT: f 9 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8341 (mpp) REVERT: f 35 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7180 (mttp) REVERT: f 91 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.6833 (mmm160) REVERT: f 93 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7670 (mtpp) REVERT: d 50 GLU cc_start: 0.8335 (mp0) cc_final: 0.7776 (tp30) REVERT: d 124 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8491 (mt) REVERT: d 183 LYS cc_start: 0.7808 (mmmt) cc_final: 0.6833 (ttpp) REVERT: d 206 LYS cc_start: 0.7401 (tttm) cc_final: 0.7019 (tmtm) REVERT: I 45 MET cc_start: 0.5723 (tpp) cc_final: 0.4626 (ttp) REVERT: t 36 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8245 (t) REVERT: r 38 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8739 (mtmm) REVERT: q 55 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7529 (mt) REVERT: l 40 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8762 (p) REVERT: l 43 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7453 (tttt) REVERT: l 44 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.6685 (mmtp) REVERT: k 79 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8406 (tp) REVERT: k 82 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6761 (mt) REVERT: k 126 LYS cc_start: 0.7972 (tttt) cc_final: 0.7614 (mmmt) REVERT: D 89 MET cc_start: 0.8888 (mmt) cc_final: 0.8467 (mmp) REVERT: J 1 MET cc_start: 0.2394 (mtt) cc_final: 0.1023 (ttt) outliers start: 90 outliers final: 50 residues processed: 383 average time/residue: 0.5731 time to fit residues: 266.4700 Evaluate side-chains 399 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 332 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 7 ARG Chi-restraints excluded: chain u residue 69 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 2 SER Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain e residue 149 LYS Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 38 LYS Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain l residue 17 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 125 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 324 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 208 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 153 HIS o 40 GLN h 91 GLN f 14 GLN f 99 GLN e 13 GLN e 78 ASN d 116 GLN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.144058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.123255 restraints weight = 52686.441| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 0.73 r_work: 0.2831 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 51545 Z= 0.221 Angle : 0.619 9.044 77067 Z= 0.322 Chirality : 0.038 0.287 9836 Planarity : 0.005 0.062 4146 Dihedral : 23.629 179.249 25785 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.93 % Favored : 96.86 % Rotamer: Outliers : 4.86 % Allowed : 20.33 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.19), residues: 1878 helix: 1.11 (0.18), residues: 787 sheet: -0.52 (0.26), residues: 359 loop : -0.70 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 127 TYR 0.027 0.002 TYR f 4 PHE 0.015 0.002 PHE o 43 TRP 0.018 0.002 TRP C 201 HIS 0.004 0.001 HIS t 75 Details of bonding type rmsd covalent geometry : bond 0.00427 (51545) covalent geometry : angle 0.61858 (77067) hydrogen bonds : bond 0.06116 ( 2051) hydrogen bonds : angle 3.43637 ( 4198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 332 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: u 7 ARG cc_start: 0.3878 (OUTLIER) cc_final: 0.3270 (tpm170) REVERT: u 17 ARG cc_start: 0.5952 (ttp-170) cc_final: 0.5039 (ttp80) REVERT: u 21 ARG cc_start: 0.6403 (mtt180) cc_final: 0.5627 (mmt90) REVERT: u 45 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8098 (mtm-85) REVERT: u 69 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.4703 (tpp-160) REVERT: C 93 LYS cc_start: 0.7333 (tttt) cc_final: 0.6923 (tmtt) REVERT: C 100 GLN cc_start: 0.7054 (mt0) cc_final: 0.6195 (mp10) REVERT: C 131 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7240 (mtt90) REVERT: C 135 LYS cc_start: 0.7655 (mttm) cc_final: 0.7448 (mttp) REVERT: C 147 LYS cc_start: 0.8136 (mttt) cc_final: 0.7823 (mttp) REVERT: G 79 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5981 (mmm160) REVERT: G 116 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5808 (tmt) REVERT: o 83 LYS cc_start: 0.8596 (tttt) cc_final: 0.8027 (ttpt) REVERT: o 84 ARG cc_start: 0.8719 (mtp180) cc_final: 0.8444 (mtm180) REVERT: h 5 ASP cc_start: 0.8611 (t0) cc_final: 0.8391 (t70) REVERT: h 8 SER cc_start: 0.9257 (p) cc_final: 0.8816 (m) REVERT: h 80 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8533 (mtp180) REVERT: f 9 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8371 (mpp) REVERT: f 35 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7175 (mttp) REVERT: f 91 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6869 (mmm160) REVERT: d 50 GLU cc_start: 0.8288 (mp0) cc_final: 0.7740 (tp30) REVERT: d 124 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8492 (mt) REVERT: d 183 LYS cc_start: 0.7782 (mmmt) cc_final: 0.6811 (ttpp) REVERT: d 206 LYS cc_start: 0.7393 (tttm) cc_final: 0.7008 (tmtm) REVERT: I 45 MET cc_start: 0.5741 (tpp) cc_final: 0.4648 (ttp) REVERT: t 36 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8221 (t) REVERT: r 38 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8746 (mtmm) REVERT: q 55 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7546 (mt) REVERT: l 40 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8749 (p) REVERT: l 43 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7455 (tttt) REVERT: l 44 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6665 (mmtp) REVERT: k 79 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8373 (tp) REVERT: k 82 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6733 (mt) REVERT: k 126 LYS cc_start: 0.7965 (tttt) cc_final: 0.7634 (mmmt) REVERT: D 89 MET cc_start: 0.8879 (mmt) cc_final: 0.8466 (mmp) REVERT: J 1 MET cc_start: 0.2463 (mtt) cc_final: 0.1060 (ttt) outliers start: 76 outliers final: 46 residues processed: 371 average time/residue: 0.5713 time to fit residues: 256.4032 Evaluate side-chains 392 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 329 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 7 ARG Chi-restraints excluded: chain u residue 69 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 38 LYS Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 51 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain l residue 17 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain J residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 192 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 153 HIS o 40 GLN h 91 GLN f 14 GLN f 99 GLN e 13 GLN e 78 ASN d 116 GLN I 125 GLN k 109 ASN D 4 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.143447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.122559 restraints weight = 53003.464| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.85 r_work: 0.2810 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 51545 Z= 0.274 Angle : 0.646 7.622 77067 Z= 0.333 Chirality : 0.040 0.299 9836 Planarity : 0.005 0.061 4146 Dihedral : 23.589 179.308 25785 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.98 % Favored : 96.81 % Rotamer: Outliers : 4.80 % Allowed : 20.65 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.19), residues: 1878 helix: 1.05 (0.18), residues: 785 sheet: -0.51 (0.26), residues: 359 loop : -0.70 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 118 TYR 0.024 0.002 TYR f 4 PHE 0.016 0.002 PHE o 43 TRP 0.016 0.002 TRP C 201 HIS 0.004 0.001 HIS k 24 Details of bonding type rmsd covalent geometry : bond 0.00529 (51545) covalent geometry : angle 0.64617 (77067) hydrogen bonds : bond 0.06166 ( 2051) hydrogen bonds : angle 3.45301 ( 4198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 332 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: u 7 ARG cc_start: 0.3716 (OUTLIER) cc_final: 0.3252 (tpm170) REVERT: u 17 ARG cc_start: 0.5978 (ttp-170) cc_final: 0.5066 (ttp80) REVERT: u 21 ARG cc_start: 0.6403 (mtt180) cc_final: 0.5663 (mmt90) REVERT: u 45 ARG cc_start: 0.8302 (mtp180) cc_final: 0.8093 (mtm-85) REVERT: u 69 ARG cc_start: 0.4904 (OUTLIER) cc_final: 0.4606 (tpp-160) REVERT: C 93 LYS cc_start: 0.7348 (tttt) cc_final: 0.6929 (tmtt) REVERT: C 100 GLN cc_start: 0.7063 (mt0) cc_final: 0.6191 (mp10) REVERT: C 131 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7223 (mtt90) REVERT: C 147 LYS cc_start: 0.8126 (mttt) cc_final: 0.7803 (mttp) REVERT: G 41 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6580 (tmmt) REVERT: G 79 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.6006 (mmm160) REVERT: G 116 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.4469 (tmt) REVERT: o 83 LYS cc_start: 0.8633 (tttt) cc_final: 0.8139 (ttpt) REVERT: o 84 ARG cc_start: 0.8725 (mtp180) cc_final: 0.8454 (mtm180) REVERT: h 80 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8535 (mtp180) REVERT: f 9 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8386 (mpp) REVERT: f 35 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7134 (mttp) REVERT: f 91 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6846 (mmm160) REVERT: f 93 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7662 (mtpp) REVERT: d 50 GLU cc_start: 0.8288 (mp0) cc_final: 0.7744 (tp30) REVERT: d 124 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8497 (mt) REVERT: d 183 LYS cc_start: 0.7783 (mmmt) cc_final: 0.6832 (ttpp) REVERT: d 184 ARG cc_start: 0.8023 (ptt90) cc_final: 0.7573 (ptt90) REVERT: d 206 LYS cc_start: 0.7389 (tttm) cc_final: 0.6995 (tmtm) REVERT: I 45 MET cc_start: 0.5735 (tpp) cc_final: 0.4635 (ttp) REVERT: t 36 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8225 (t) REVERT: r 38 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8754 (mtmm) REVERT: q 55 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7535 (mt) REVERT: l 40 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8750 (p) REVERT: l 43 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7375 (tttt) REVERT: l 44 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6631 (mmtp) REVERT: k 79 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8333 (tp) REVERT: k 82 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6759 (mt) REVERT: k 126 LYS cc_start: 0.7974 (tttt) cc_final: 0.7636 (mmmt) REVERT: D 89 MET cc_start: 0.8876 (mmt) cc_final: 0.8460 (mmp) REVERT: J 1 MET cc_start: 0.2561 (mtt) cc_final: 0.1141 (ttt) outliers start: 75 outliers final: 42 residues processed: 375 average time/residue: 0.5781 time to fit residues: 261.3666 Evaluate side-chains 387 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 327 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 7 ARG Chi-restraints excluded: chain u residue 69 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 88 ARG Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 91 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain e residue 117 GLU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 160 GLU Chi-restraints excluded: chain d residue 177 LYS Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 38 LYS Chi-restraints excluded: chain r residue 62 SER Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain l residue 17 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain J residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 303 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN G 153 HIS o 40 GLN h 91 GLN f 14 GLN f 99 GLN e 13 GLN e 78 ASN d 116 GLN I 125 GLN k 109 ASN D 4 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.144253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123436 restraints weight = 52807.058| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 0.74 r_work: 0.2835 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 51545 Z= 0.220 Angle : 0.617 9.939 77067 Z= 0.321 Chirality : 0.037 0.287 9836 Planarity : 0.005 0.062 4146 Dihedral : 23.608 179.263 25785 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.93 % Favored : 96.86 % Rotamer: Outliers : 4.73 % Allowed : 20.78 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1878 helix: 1.08 (0.18), residues: 793 sheet: -0.52 (0.26), residues: 359 loop : -0.67 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 127 TYR 0.028 0.002 TYR r 51 PHE 0.015 0.002 PHE o 43 TRP 0.017 0.002 TRP C 201 HIS 0.004 0.001 HIS e 90 Details of bonding type rmsd covalent geometry : bond 0.00423 (51545) covalent geometry : angle 0.61661 (77067) hydrogen bonds : bond 0.06053 ( 2051) hydrogen bonds : angle 3.43263 ( 4198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11168.08 seconds wall clock time: 191 minutes 12.06 seconds (11472.06 seconds total)